|
| Status |
Public on Mar 06, 2018 |
| Title |
MEF_4H8_KO_rep1_20446 |
| Sample type |
SRA |
| |
|
| Source name |
primary mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
tissue: primary mouse embryonic fibroblasts
genotype: Supt5hFl/- Rosa26ERT2-cre/+
antibody: RNA Pol II (4H8)
|
| Treatment protocol |
Primary MEFs were treated with 2 uM 4-HT for 72h and then harvested for all downstream applications.
|
| Growth protocol |
Primary MEFs were prepared from d13.5 Supt5hFl/+Rosa26ERT2-cre/+ and Rosa26ERT2-cre/+ embryos and cultured in complete DMEM medium to passage 3.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIPseq and ChIP-qPCR were performed as described without modifications (Pavri et al., 2010). In short, 20x10^6 cells were crosslinked with 1% HCHO for 10 min at 37 degree. After quenching with 0,125 M glycine, cells were sonicated with the Diagenode Bioruptor sonication machine.
After chromatin-immunprecipitation, samples were end-repaired with the Epicenter End-Repair Kit. After A-tailing the samples with Klenow (exo-) enzyme, NEXTflex adapters were ligated to the samples and then purified with AMPure XP beads. PCR amplification of the libraries was performed with the Phusion-HF enzyme and the NEXTflex primer mix.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Adapters were trimmed from the 3' ends of the reads with cutadapt v1.10.
Trimmed reads larger than 18nt were aligned to the genome using bowtie v1.0.0 (-v 2 --best --strata --tryhard -m 1)
genome build: NCBI mm9
processed data files format and content: bigWig of rpm-normalized read densities
|
| |
|
| Submission date |
Oct 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tobias Neumann |
| Organization name |
IMP
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE106313 |
Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window in elongation |
|
| Relations |
| BioSample |
SAMN07946554 |
| SRA |
SRX3342570 |
